First I must say, this is one fantastic game. Congrats to Stardock on all of the great reviews, the game absolutely deserves it.
My suggestion has to do with how intelligence operations occur in the game. I overall like the way it happens, with you setting a budget for covert ops for each civilizations and gradually you penetrate deeper into that civilization. However, it doesn't seem to make sense that once you have reached an advanced level of intelligence information, that you can stop spending money on covert ops and still keep the same high level of intelligence that you worked up to. Naturally enemy governments are doing counterintelligence to find how they have been compromised and would begin to counter your intelligence operations.
Why not have your level of intelligence on each civilizations gradually degrade if you stop funding covert ops in that nation. I think it is a bit more realistic and would add more strategy into planning for wars.